gmx eneconv#

Synopsis#

gmx eneconv [-f [<.edr> [...]]] [-o [<.edr>]] [-b <real>] [-e <real>]
            [-dt <real>] [-offset <real>] [-[no]settime] [-[no]sort]
            [-[no]rmdh] [-scalefac <real>] [-[no]error]

Description#

With multiple files specified for the -f option:

Concatenates several energy files in sorted order. In the case of double time frames, the one in the later file is used. By specifying -settime you will be asked for the start time of each file. The input files are taken from the command line, such that the command gmx eneconv -f *.edr -o fixed.edr should do the trick.

With one file specified for -f:

Reads one energy file and writes another, applying the -dt, -offset, -t0 and -settime options and converting to a different format if necessary (indicated by file extensions).

-settime is applied first, then -dt/-offset followed by -b and -e to select which frames to write.

Options#

Options to specify input files:

-f [<.edr> […]] (ener.edr): Energy file

Options to specify output files:

-o [<.edr>] (fixed.edr): Energy file

Other options:

-b <real> (-1): First time to use
-e <real> (-1): Last time to use
-dt <real> (0): Only write out frame when t MOD dt = offset
-offset <real> (0): Time offset for -dt option
-[no]settime (no): Change starting time interactively
-[no]sort (yes): Sort energy files (not frames)
-[no]rmdh (no): Remove free energy block data
-scalefac <real> (1): Multiply energy component by this factor
-[no]error (yes): Stop on errors in the file

Known Issues#

When combining trajectories the sigma and E^2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way.